The single-cell literature catalogs cell states as validated marker-gene programs — a sparse, compositional prior. Conventional embedding methods do not leverage this prior and learn cell-state structure de novo from the expression matrix, producing dense dimensions needing post-hoc interpretation and batch correction. Here we show coding agents can author single-cell embedding models directly from the literature. Given a scenario that focuses this literature lens on a chosen biological subdomain, the agent edits a structured Python template, curating named, literature-cited gene programs and composing them into axes, without a gene-set database, training, or sight of the data. Across mouse and human tissues these zero-shot embeddings are competitive in biological quality with conventional, foundation-model, and program-informed baselines, batch-robust by construction and reproducible across runs, complementing data-driven embeddings. Because each dimension is a named, cited gene program, the embedding is interpretable and auditable, and its composable axes can be steered into a developmental tree.
Niklas Brunn, S. M. Krißmer, Maximilian Frosch et al.· bioRxiv· 0 citations
The mouse epidermis harbors two key resident immune populations—dendritic epidermal T cells (DETCs), a subset of invariant γδ T cells, and Langerhans cells (LCs), specialized tissue-resident macrophages—both of which play critical roles in immune surveillance, barrier integrity, and tissue homeostasis. While their fetal origin has been defined, the mechanisms governing their postnatal maturation remain poorly understood. Here, we present a combined immunophenotypic and single-cell transcriptomic map of DETC and LC development from late embryogenesis through adulthood in mice. We delineate distinct differentiation trajectories characterized by dynamic changes in morphology, proliferation, and transcriptional programming. Using γδ T cell deficient mice, we show that LC maturation proceeds independently of canonical γδDETCs, likely due to compensatory αβDETCs. Analysis of germfree mice and wildlings further demonstrates that the postnatal DETC and LC differentiation is independent of microbial colonization. Comparative analysis with developing human epidermis reveals partially conserved differentiation programs. Together, our findings define core principles underlying establishment of the epidermal immune niche.
D. Obwegs, Alexander Oschwald, L. Koetter et al.· Science Advances· 0 citations
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